Multiple sequence alignment - TraesCS6A01G171700

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6A01G171700 chr6A 100.000 2531 0 0 1 2531 182421823 182419293 0.000000e+00 4674
1 TraesCS6A01G171700 chr6A 94.020 2542 104 13 1 2531 137494906 137492402 0.000000e+00 3808
2 TraesCS6A01G171700 chr3B 96.260 2540 85 7 1 2531 473234220 473236758 0.000000e+00 4156
3 TraesCS6A01G171700 chr2A 96.336 2538 64 7 1 2531 778647325 778649840 0.000000e+00 4145
4 TraesCS6A01G171700 chr7A 95.671 2541 83 10 1 2531 126147078 126149601 0.000000e+00 4058
5 TraesCS6A01G171700 chr7B 95.347 2536 111 5 1 2531 51882338 51884871 0.000000e+00 4023
6 TraesCS6A01G171700 chr7B 85.905 1575 179 29 996 2531 73167298 73168868 0.000000e+00 1639
7 TraesCS6A01G171700 chr6B 95.191 2537 96 9 1 2531 48078038 48080554 0.000000e+00 3986
8 TraesCS6A01G171700 chr4B 94.683 2539 125 7 1 2531 321540568 321543104 0.000000e+00 3932
9 TraesCS6A01G171700 chr4B 94.419 2222 108 12 1 2209 587096929 587099147 0.000000e+00 3402
10 TraesCS6A01G171700 chr4B 84.047 1285 159 32 1288 2531 43574172 43572893 0.000000e+00 1195
11 TraesCS6A01G171700 chr4B 96.154 286 10 1 2246 2531 587099150 587099434 1.370000e-127 466
12 TraesCS6A01G171700 chr3A 96.364 2283 74 7 1 2276 153361218 153363498 0.000000e+00 3747
13 TraesCS6A01G171700 chr7D 85.415 1577 185 31 996 2531 83758294 83759866 0.000000e+00 1596


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G171700 chr6A 182419293 182421823 2530 True 4674 4674 100.0000 1 2531 1 chr6A.!!$R2 2530
1 TraesCS6A01G171700 chr6A 137492402 137494906 2504 True 3808 3808 94.0200 1 2531 1 chr6A.!!$R1 2530
2 TraesCS6A01G171700 chr3B 473234220 473236758 2538 False 4156 4156 96.2600 1 2531 1 chr3B.!!$F1 2530
3 TraesCS6A01G171700 chr2A 778647325 778649840 2515 False 4145 4145 96.3360 1 2531 1 chr2A.!!$F1 2530
4 TraesCS6A01G171700 chr7A 126147078 126149601 2523 False 4058 4058 95.6710 1 2531 1 chr7A.!!$F1 2530
5 TraesCS6A01G171700 chr7B 51882338 51884871 2533 False 4023 4023 95.3470 1 2531 1 chr7B.!!$F1 2530
6 TraesCS6A01G171700 chr7B 73167298 73168868 1570 False 1639 1639 85.9050 996 2531 1 chr7B.!!$F2 1535
7 TraesCS6A01G171700 chr6B 48078038 48080554 2516 False 3986 3986 95.1910 1 2531 1 chr6B.!!$F1 2530
8 TraesCS6A01G171700 chr4B 321540568 321543104 2536 False 3932 3932 94.6830 1 2531 1 chr4B.!!$F1 2530
9 TraesCS6A01G171700 chr4B 587096929 587099434 2505 False 1934 3402 95.2865 1 2531 2 chr4B.!!$F2 2530
10 TraesCS6A01G171700 chr4B 43572893 43574172 1279 True 1195 1195 84.0470 1288 2531 1 chr4B.!!$R1 1243
11 TraesCS6A01G171700 chr3A 153361218 153363498 2280 False 3747 3747 96.3640 1 2276 1 chr3A.!!$F1 2275
12 TraesCS6A01G171700 chr7D 83758294 83759866 1572 False 1596 1596 85.4150 996 2531 1 chr7D.!!$F1 1535

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
66 67 1.733041 TTCTTGCCGTCGAGAAGCG 60.733 57.895 0.0 0.0 37.7 4.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1915 1943 1.148273 GGTGGGTTCTGTGCTGTCA 59.852 57.895 0.0 0.0 0.0 3.58 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 67 1.733041 TTCTTGCCGTCGAGAAGCG 60.733 57.895 0.00 0.0 37.70 4.68
362 364 6.377996 TGCTACAATTGCAAGGATGACTTAAT 59.622 34.615 4.94 0.0 37.29 1.40
448 452 5.246203 TGGTATCTAGCTTGTCTTTGTGTCT 59.754 40.000 0.00 0.0 0.00 3.41
454 460 4.737054 AGCTTGTCTTTGTGTCTTGTTTG 58.263 39.130 0.00 0.0 0.00 2.93
542 550 8.847196 TCTAGACGCTAATAATATGTGACTGTT 58.153 33.333 0.00 0.0 0.00 3.16
561 573 4.252878 TGTTTGCACACTATGATGACGAT 58.747 39.130 4.37 0.0 0.00 3.73
658 670 9.065871 GCTGGCTTATAAATTATAGCAATTTCG 57.934 33.333 12.79 0.0 32.64 3.46
1078 1096 5.294734 TCTGATGAGTGCCATTATGCTTA 57.705 39.130 0.00 0.0 35.17 3.09
1459 1477 4.397103 TGAAGCTTCATCCATTGCTACTTG 59.603 41.667 25.16 0.0 35.09 3.16
1612 1637 9.944663 GTTGTTTATGTTGTAGAATTGTCTTGA 57.055 29.630 0.00 0.0 35.12 3.02
1687 1712 1.354101 TACCGATCAAGGTTGGGTGT 58.646 50.000 0.00 0.0 43.00 4.16
1715 1742 3.708563 ACAAATGTGTTAGGTGTGTGC 57.291 42.857 0.00 0.0 32.58 4.57
1915 1943 5.068591 GTCAAAAGTATCACTTGGGTGGTTT 59.931 40.000 0.00 0.0 43.17 3.27
1999 2027 7.554476 AGCCTGAAATATTGTAGAAAGGTCTTC 59.446 37.037 0.00 0.0 35.12 2.87
2232 2268 2.135664 ACTTCGAACGAGTGGACAAG 57.864 50.000 0.00 0.0 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
448 452 5.242615 TCAAGGCAGCAACATATACAAACAA 59.757 36.000 0.00 0.00 0.00 2.83
454 460 6.038603 TGAAATCTCAAGGCAGCAACATATAC 59.961 38.462 0.00 0.00 0.00 1.47
542 550 3.197265 CCATCGTCATCATAGTGTGCAA 58.803 45.455 0.00 0.00 0.00 4.08
561 573 4.634012 AGAGTGTAAATAAGTGGCACCA 57.366 40.909 15.27 2.54 0.00 4.17
658 670 9.713740 TGCACATGAAAACAAAACAAAATATTC 57.286 25.926 0.00 0.00 0.00 1.75
678 691 3.517100 AGTACACTTCAGATCCTGCACAT 59.483 43.478 0.00 0.00 0.00 3.21
951 965 4.224370 GGTAATTCTAGGAGGTGTGGTTGA 59.776 45.833 0.00 0.00 0.00 3.18
1459 1477 3.703052 TCGGGTATAGGTTCTGGTTTCTC 59.297 47.826 0.00 0.00 0.00 2.87
1612 1637 1.156736 GTGTGTGCCATCTAACGCTT 58.843 50.000 0.00 0.00 0.00 4.68
1715 1742 1.229975 TGAACTGCATGTCAGGTGCG 61.230 55.000 17.61 0.00 44.28 5.34
1803 1831 1.265236 GGGACATGCAACCCATTTGA 58.735 50.000 18.12 0.00 44.96 2.69
1915 1943 1.148273 GGTGGGTTCTGTGCTGTCA 59.852 57.895 0.00 0.00 0.00 3.58
1999 2027 1.204941 CACTGACCCTTAGTCTTCCGG 59.795 57.143 0.00 0.00 46.46 5.14
2051 2084 4.014569 TGATTCGACATTGGGTCTTCAA 57.985 40.909 0.00 0.00 44.68 2.69
2232 2268 1.963747 CGCAAGAACATTCCGGAAAC 58.036 50.000 23.08 12.81 43.02 2.78


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.